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- PDB-2oi2: Streptococcus pneumoniae Mevalonate Kinase in Complex with Diphos... -

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Basic information

Entry
Database: PDB / ID: 2oi2
TitleStreptococcus pneumoniae Mevalonate Kinase in Complex with Diphosphomevalonate
ComponentsMevalonate kinase
KeywordsTRANSFERASE / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / isoprenoid biosynthetic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Mevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...Mevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DP6 / Mevalonate kinase / Mevalonate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsAndreassi, J.L. / Bilder, P.W. / Vetting, M.W. / Roderick, S.L. / Leyh, T.S.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonate.
Authors: Andreassi, J.L. / Bilder, P.W. / Vetting, M.W. / Roderick, S.L. / Leyh, T.S.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7963
Polymers31,4641
Non-polymers3322
Water1,04558
1
A: Mevalonate kinase
hetero molecules

A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5936
Polymers62,9282
Non-polymers6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)101.597, 101.597, 83.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is dimeric. The dimer is formed by a crystallographic twofold rotation.

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Components

#1: Protein Mevalonate kinase


Mass: 31464.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: mvk / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8DR51, UniProt: A0A0H2UNK6*PLUS, mevalonate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES, KCl, DTT, AMPPNP, MgCl2, Diphosphomevalonate, PEG, formate, pH 7.5, SITTING DROP UNDER OIL, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 2004 / Details: Osmic Blue
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30.89 Å / Num. all: 16144 / Num. obs: 16144 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.271 / % possible all: 81.2

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Processing

Software
NameVersionClassification
CNS1refinement
CTRdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 501748.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 787 4.9 %RANDOM
Rwork0.211 ---
obs0.211 16144 92 %-
all-16144 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.119 Å2 / ksol: 0.386215 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.18 Å25.79 Å20 Å2
2--0.18 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 19 58 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 90 3.8 %
Rwork0.272 2250 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dpm.pardpm.top

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